X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=ec03b859b49a66f09151777f4b5422246403778e;hb=012fc200ee0d124003524855ac7cd50be4b7456c;hp=8a94a895aadded33776f94672513d8ec8d7cb52e;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 8a94a89..ec03b85 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -24,6 +24,10 @@ import java.awt.*;
 
 import java.util.*;
 
+import java.awt.image.*;
+import javax.swing.*;
+import javax.swing.JOptionPane;
+
 
 /**
  * DOCUMENT ME!
@@ -34,10 +38,23 @@ import java.util.*;
 public class FeatureRenderer
 {
     AlignViewport av;
-    SequenceGroup currentSequenceGroup = null;
-    SequenceGroup[] allGroups = null;
     Color resBoxColour;
-    Graphics graphics;
+    float transparency = 1.0f;
+    FontMetrics fm;
+    int charOffset;
+
+    Hashtable featureColours = new Hashtable();
+
+
+    // A higher level for grouping features of a
+   // particular type
+    Hashtable featureGroups = null;
+
+    // This is actually an Integer held in the hashtable,
+    // Retrieved using the key feature type
+    Object currentColour;
+
+    String [] renderOrder;
 
     /**
      * Creates a new FeatureRenderer object.
@@ -49,6 +66,81 @@ public class FeatureRenderer
         this.av = av;
     }
 
+    public void transferSettings(FeatureRenderer fr)
+    {
+      renderOrder = fr.renderOrder;
+      featureGroups = fr.featureGroups;
+      featureColours = fr.featureColours;
+      transparency =  fr.transparency;
+    }
+
+    BufferedImage offscreenImage;
+    boolean offscreenRender = false;
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+    {
+      return new Color( findFeatureColour (initialCol.getRGB(),
+                        seq, res ));
+    }
+
+    /**
+     * This is used by the Molecule Viewer and Overview to
+     * get the accurate colourof the rendered sequence
+     */
+    public int findFeatureColour(int initialCol, SequenceI seq, int column)
+    {
+      if(!av.showSequenceFeatures)
+        return initialCol;
+
+      if(seq!=lastSeq)
+      {
+        lastSeq = seq;
+        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+        if(sequenceFeatures==null)
+          return initialCol;
+
+        sfSize = sequenceFeatures.length;
+      }
+
+      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
+        return Color.white.getRGB();
+
+
+      //Only bother making an offscreen image if transparency is applied
+      if(transparency!=1.0f && offscreenImage==null)
+      {
+        offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
+      }
+
+      currentColour = null;
+
+      offscreenRender = true;
+
+      if(offscreenImage!=null)
+      {
+        offscreenImage.setRGB(0,0,initialCol);
+        drawSequence(offscreenImage.getGraphics(),
+                     lastSeq,
+                     column,column,0);
+
+        return offscreenImage.getRGB(0,0);
+      }
+      else
+      {
+        drawSequence(null,
+                    lastSeq,
+                    lastSeq.findPosition(column),
+                    -1, -1);
+
+        if (currentColour == null)
+          return initialCol;
+        else
+          return  ((Integer)currentColour).intValue();
+      }
+
+
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -62,76 +154,428 @@ public class FeatureRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-        int start, int end, int x1, int y1, int width, int height)
+   // String type;
+   // SequenceFeature sf;
+    SequenceI lastSeq;
+    SequenceFeature [] sequenceFeatures;
+    int sfSize, sfindex, spos, epos;
+
+    public void drawSequence(Graphics g, SequenceI seq,
+                             int start, int end, int y1)
+    {
+      if ( seq.getDatasetSequence().getSequenceFeatures() == null
+          || seq.getDatasetSequence().getSequenceFeatures().length==0)
+        return;
+
+      if(g!=null)
+        fm = g.getFontMetrics();
+
+
+      if (av.featuresDisplayed == null
+          || renderOrder==null
+          || newFeatureAdded)
+       {
+         findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
+
+         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+         sfSize = sequenceFeatures.length;
+       }
+
+       if(lastSeq==null || seq!=lastSeq)
+      {
+        lastSeq = seq;
+        sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+        sfSize = sequenceFeatures.length;
+      }
+
+
+      if (transparency != 1 && g!=null)
+      {
+        Graphics2D g2 = (Graphics2D) g;
+        g2.setComposite(
+            AlphaComposite.getInstance(
+                AlphaComposite.SRC_OVER, transparency));
+      }
+
+      if(!offscreenRender)
+      {
+        spos = lastSeq.findPosition(start);
+        epos = lastSeq.findPosition(end);
+      }
+
+
+      String type;
+      for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
+       {
+        type =  renderOrder[renderIndex];
+
+        if(!av.featuresDisplayed.containsKey(type))
+          continue;
+
+        // loop through all features in sequence to find
+        // current feature to render
+        for (sfindex = 0; sfindex < sfSize; sfindex++)
+        {
+          if(sequenceFeatures.length<=sfindex)
+          {
+            continue;
+          }
+          if (!sequenceFeatures[sfindex].type.equals(type))
+            continue;
+
+          if (featureGroups != null
+              && sequenceFeatures[sfindex].featureGroup != null
+              &&
+              featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+              &&
+              ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
+              booleanValue())
+          {
+            continue;
+          }
+
+          if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
+                            || sequenceFeatures[sfindex].getEnd() < spos))
+            continue;
+
+          if (offscreenRender && offscreenImage==null)
+          {
+            if (sequenceFeatures[sfindex].begin <= start &&
+                sequenceFeatures[sfindex].end  >= start)
+            {
+              currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                 type);
+            }
+          }
+          else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+          {
+
+            renderFeature(g, seq,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          new Color( ( (Integer) av.featuresDisplayed.get(
+                sequenceFeatures[sfindex].type)).intValue()),
+                          start, end, y1);
+            renderFeature(g, seq,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          new Color( ( (Integer) av.featuresDisplayed.get(
+                sequenceFeatures[sfindex].type)).intValue()),
+                          start, end, y1);
+
+          }
+          else
+            renderFeature(g, seq,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          getColour(sequenceFeatures[sfindex].type),
+                          start, end, y1);
+
+
+        }
+
+      }
+
+        if(transparency!=1.0f && g!=null)
+        {
+          Graphics2D g2 = (Graphics2D) g;
+          g2.setComposite(
+              AlphaComposite.getInstance(
+                  AlphaComposite.SRC_OVER, 1.0f));
+        }
+    }
+
+
+    char s;
+    int i;
+    void renderFeature(Graphics g, SequenceI seq,
+                       int fstart, int fend, Color featureColour, int start, int end,  int y1)
     {
-        Vector features = seq.getSequenceFeatures();
-        Enumeration e = features.elements();
 
-        while (e.hasMoreElements())
+      if (((fstart <= end) && (fend >= start)))
+      {
+        if (fstart < start)
+        { // fix for if the feature we have starts before the sequence start,
+          fstart = start; // but the feature end is still valid!!
+        }
+
+        if (fend >= end)
         {
-            SequenceFeature sf = (SequenceFeature) e.nextElement();
+          fend = end;
+        }
+          int pady = (y1 + av.charHeight) - av.charHeight / 5;
+          for (i = fstart; i <= fend; i++)
+          {
+            s = seq.getSequence().charAt(i);
 
-            if (sf.getStart() > seq.getEnd())
+            if (jalview.util.Comparison.isGap(s))
             {
-                continue;
+              continue;
             }
 
-            int fstart = seq.findIndex(sf.getStart()) - 1;
-            int fend = seq.findIndex(sf.getEnd()) - 1;
+            g.setColor(featureColour);
+
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
+
+            if(offscreenRender || !av.validCharWidth)
+              continue;
+
+            g.setColor(Color.white);
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+            g.drawString(String.valueOf(s),
+                         charOffset + (av.charWidth * (i - start)),
+                         pady);
+
+          }
+      }
+    }
+
+
+    boolean newFeatureAdded = false;
+
+    public void featuresAdded()
+    {
+      findAllFeatures();
+    }
+
+   boolean findingFeatures = false;
+   synchronized void findAllFeatures()
+   {
+      newFeatureAdded = false;
+
+      if(findingFeatures)
+      {
+        newFeatureAdded = true;
+        return;
+      }
+
+      findingFeatures = true;
+      jalview.schemes.UserColourScheme ucs = new
+          jalview.schemes.UserColourScheme();
+
+      if(av.featuresDisplayed==null)
+        av.featuresDisplayed = new Hashtable();
 
-            if (((fstart <= end) && (fend >= start)))
+      av.featuresDisplayed.clear();
+
+      Vector allfeatures = new Vector();
+      for (int i = 0; i < av.alignment.getHeight(); i++)
+      {
+        SequenceFeature [] features
+            = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+
+        if (features == null)
+          continue;
+
+        int index = 0;
+        while (index < features.length)
+        {
+          if (!av.featuresDisplayed.containsKey(features[index].getType()))
+          {
+            if(!(features[index].begin == 0 && features[index].end ==0))
             {
-                if (fstart < start)
-                { // fix for if the feature we have starts before the sequence start,
-                    fstart = start; // but the feature end is still valid!!
-                }
-
-                if (fend >= end)
-                {
-                    fend = end;
-                }
-
-                if (fstart == fend)
-                {
-                    g.setColor(Color.red);
-                    g.fillRoundRect((fstart - start) * width, y1, width,
-                        height, 4, 4);
-                    g.setColor(Color.white);
-
-                    char s = seq.getSequence().charAt(fstart);
-                    FontMetrics fm = g.getFontMetrics();
-                    int charOffset = (width - fm.charWidth(s)) / 2;
-                    int pady = height / 5;
-                    g.drawString(String.valueOf(s),
-                        charOffset + x1 + (width * (fstart - start)),
-                        (y1 + height) - pady);
-                }
-                else
-                {
-                    for (int i = fstart; i <= fend; i++)
-                    {
-                        char s = seq.getSequence().charAt(i);
-
-                        if (jalview.util.Comparison.isGap(s))
-                        {
-                            continue;
-                        }
-
-                        g.setColor(Color.blue);
-                        g.fillRect((i - start) * width, y1, width, height);
-
-                        g.setColor(Color.white);
-
-                        FontMetrics fm = g.getFontMetrics();
-                        int charOffset = (width - fm.charWidth(s)) / 2;
-                        int pady = height / 5;
-                        g.drawString(String.valueOf(s),
-                            charOffset + x1 + (width * (i - start)),
-                            (y1 + height) - pady);
-                    }
-                }
+              // If beginning and end are 0, the feature is for the whole sequence
+              // and we don't want to render the feature in the normal way
+
+              if (getColour(features[index].getType()) == null)
+              {
+                 featureColours.put(features[index].getType(),
+                                   ucs.createColourFromName(features[index].
+                    getType()));
+              }
+
+              av.featuresDisplayed.put(features[index].getType(),
+                                       new Integer(getColour(features[index].
+                  getType()).getRGB()));
+              allfeatures.addElement(features[index].getType());
             }
+          }
+          index++;
+        }
+      }
+
+      renderOrder = new String[allfeatures.size()];
+      Enumeration en = allfeatures.elements();
+      int i = allfeatures.size()-1;
+      while(en.hasMoreElements())
+      {
+        renderOrder[i] = en.nextElement().toString();
+        i--;
+      }
+
+      findingFeatures = false;
+    }
+
+    public Color getColour(String featureType)
+    {
+      Color colour = (Color)featureColours.get(featureType);
+      return colour;
+    }
+
+
+    static String lastFeatureAdded;
+    static String lastFeatureGroupAdded;
+    static String lastDescriptionAdded;
+
+    public boolean createNewFeatures(SequenceI[] sequences,
+                                  SequenceFeature [] features)
+    {
+
+      JPanel bigPanel = new JPanel(new BorderLayout());
+      JComboBox name = new JComboBox();
+      JComboBox source = new JComboBox();
+      JTextArea description = new JTextArea(3,25);
+
+      JPanel panel = new JPanel(new GridLayout(2, 2));
+      panel.add(new JLabel("New Sequence Feature Name: ",JLabel.RIGHT));
+      panel.add(name);
+      panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
+      panel.add(source);
+      name.setEditable(true);
+      source.setEditable(true);
+
+      bigPanel.add(panel, BorderLayout.NORTH);
+      panel = new JPanel();
+      panel.add(new JLabel("Description: ", JLabel.RIGHT));
+      description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+      description.setLineWrap(true);
+      panel.add(new JScrollPane(description));
+      bigPanel.add(panel, BorderLayout.CENTER);
+
+
+      Enumeration en;
+      if (av.featuresDisplayed != null)
+      {
+        en = av.featuresDisplayed.keys();
+        while (en.hasMoreElements())
+        {
+          name.addItem(en.nextElement().toString());
+        }
+      }
+
+      if (featureGroups != null)
+      {
+        en = featureGroups.keys();
+        while (en.hasMoreElements())
+        {
+          source.addItem(en.nextElement().toString());
+        }
+      }
+
+      if (lastFeatureAdded == null)
+        if (features[0].type != null)
+          lastFeatureAdded = features[0].type;
+        else
+          lastFeatureAdded = "feature_1";
+
+      if (lastFeatureGroupAdded == null)
+        if (features[0].featureGroup != null)
+          lastFeatureGroupAdded = features[0].featureGroup;
+        else
+          lastFeatureAdded = "Jalview";
+
+
+      name.setSelectedItem(lastFeatureAdded);
+      source.setSelectedItem(lastFeatureGroupAdded);
+      description.setText(
+          lastDescriptionAdded == null ?
+          features[0].description : lastDescriptionAdded);
+
+
+      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          bigPanel, "Create New Sequence Feature(s)",
+          JOptionPane.OK_CANCEL_OPTION);
+
+
+      if(reply==JOptionPane.OK_OPTION
+         && name.getSelectedItem()!=null
+         && source.getSelectedItem()!=null)
+      {
+        lastFeatureAdded = name.getSelectedItem().toString();
+        lastFeatureGroupAdded = source.getSelectedItem().toString();
+        lastDescriptionAdded = description.getText().replaceAll("\n"," ");
+
+        jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+
+        for(int i=0; i<sequences.length; i++)
+        {
+          features[i].type = lastFeatureAdded;
+          features[i].featureGroup = lastFeatureGroupAdded;
+          features[i].description = lastDescriptionAdded;
+          sequences[i].addSequenceFeature(features[i]);
+          ffile.parseDescriptionHTML(features[i], false);
         }
+
+        if (av.featuresDisplayed == null)
+          av.featuresDisplayed = new Hashtable();
+
+        if(featureGroups==null)
+          featureGroups = new Hashtable();
+
+        featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+
+        Color col = getColour(lastFeatureAdded);
+        if(col==null)
+        {
+          col = new Color(60, 160, 115);
+          setColour(lastFeatureAdded, col);
+        }
+
+        av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col.getRGB()));
+        findAllFeatures();
+        return true;
+      }
+      else
+        return false;
+
     }
+
+    public void setColour(String featureType, Color col)
+    {
+      featureColours.put(featureType, col);
+    }
+
+    public void setTransparency(float value)
+    {
+      transparency = value;
+    }
+
+    public float getTransparency()
+    {
+      return transparency;
+    }
+
+    public void setFeaturePriority(Object [][] data)
+    {
+      // The feature table will display high priority
+      // features at the top, but theses are the ones
+      // we need to render last, so invert the data
+      if(av.featuresDisplayed!=null)
+        av.featuresDisplayed.clear();
+      else
+        av.featuresDisplayed = new Hashtable();
+
+      renderOrder = new String[data.length];
+
+      if (data.length > 0)
+        for (int i = 0; i < data.length; i++)
+        {
+          String type = data[i][0].toString();
+          setColour(type, (Color) data[i][1]);
+          if ( ( (Boolean) data[i][2]).booleanValue())
+          {
+            av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+          }
+
+          renderOrder[data.length - i - 1] = type;
+        }
+
+    }
+
+
+
+
 }